Chromosome-level genome assembly and structural variant analysis of two laboratory yeast strains from the Peterhof Genetic Collection lineage.
FLO genes
74-D694
Yeast genome
long reads
structural variant
Journal
G3 (Bethesda, Md.)
ISSN: 2160-1836
Titre abrégé: G3 (Bethesda)
Pays: England
ID NLM: 101566598
Informations de publication
Date de publication:
15 04 2021
15 04 2021
Historique:
received:
16
09
2020
accepted:
22
01
2021
pubmed:
8
3
2021
medline:
8
7
2021
entrez:
7
3
2021
Statut:
ppublish
Résumé
Thousands of yeast genomes have been sequenced with both traditional and long-read technologies, and multiple observations about modes of genome evolution for both wild and laboratory strains have been drawn from these sequences. In our study, we applied Oxford Nanopore and Illumina technologies to assemble complete genomes of two widely used members of a distinct laboratory yeast lineage, the Peterhof Genetic Collection (PGC), and investigate the structural features of these genomes including transposable element content, copy number alterations, and structural rearrangements. We identified numerous notable structural differences between genomes of PGC strains and the reference S288C strain. We discovered a substantial enrichment of mid-length insertions and deletions within repetitive coding sequences, such as in the SCH9 gene or the NUP100 gene, with possible impact of these variants on protein amyloidogenicity. High contiguity of the final assemblies allowed us to trace back the history of reciprocal unbalanced translocations between chromosomes I, VIII, IX, XI, and XVI of the PGC strains. We show that formation of hybrid alleles of the FLO genes during such chromosomal rearrangements is likely responsible for the lack of invasive growth of yeast strains. Taken together, our results highlight important features of laboratory yeast strain evolution using the power of long-read sequencing.
Identifiants
pubmed: 33677552
pii: 6129118
doi: 10.1093/g3journal/jkab029
pmc: PMC8759820
pii:
doi:
Substances chimiques
DNA Transposable Elements
0
Saccharomyces cerevisiae Proteins
0
Protein Serine-Threonine Kinases
EC 2.7.11.1
SCH9 protein, S cerevisiae
EC 2.7.11.1
Banques de données
figshare
['10.25387/g3.13635110']
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Informations de copyright
© The Author(s) 2021. Published by Oxford University Press on behalf of Genetics Society of America.
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